As we all know, when you first find the Railroad beneath the Church, Desdemona is skeptical of the player, but Deacon comes out and vouches for the player. What he says is based off what side quests you've completed and the decisions you've made.
I noticed that two pieces of Deacon's intel actually reference cut content:
https://www.youtube.com/watch?v=d_ddbZuBP6o
- "A Chinese nuclear sub. An undersea vault. And a daring rescue. That ring any bells?" (1:00)
The first part is an obvious reference to Here There Be Monsters, which is the quest that triggers this piece of intel. However, the latter two bits make no sense. Sure, you could say Here There Be Monsters has these in the metaphorical sense, but that's really stretching it. It seems to me that Here There Be Monsters must have been cut down largely before release. This is possibly related to the cut quest http://fallout.wikia.com/wiki/20_Leagues_Under_the_Sea
- "Rumor has it Salem was about to go nova. Then some stranger brokered a peace. Sound familiar?" (2:03)
Triggered by completing The Devil's Due, but is obviously referencing something else entirely. There are some inklings of evidence that Salem was initially inteded to be an actual inhabited town, but nothing solid.
Minor stuff, but I find it interesting. Cool to see "what could have been". It will be good when the GECK comes out and we can get a more thorough look at the cut content.